Hi Mark,
Yes, I have had success running many GROMACS simulations with a simple graphene sheet inside a box.
I believe I have regenerated the .tpr file from the new .mdp as the very first
command I issue is:
grompp -np $NUM_PROCS -f em.mdp -c $GRO_FILE -p $TOP_FILE -o emtopol.tpr -n
index.ndx
Please advise me on what I may be doing wrong.
Also, note that there appears to be no reference to the statement "periodic_molecules =
yes" in the GROMACS manual as I did a search in the manual for "periodic_molecules"
and the search came back empty.
Thanks.
Darrell
Date: Tue, 22 Sep 2009 15:07:03 +1000
From: Mark Abraham <mark.abra...@anu.edu.au>
Subject: Re: [gmx-users] 1-4 interaction between atoms in PBC mode
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <4ab85b77.10...@anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Darrell Koskinen wrote:
> Hi Mark,
> I did not have the statement "periodic_molecules = yes" in the .mdp
> files. I only had the statement "pbc=xyz" in the .mdp files.
>
> So, I added the "periodic_molecules = yes" statement to the .mdp files
> and ran the simulation again. However, this did not appear to resolve
> the problem as I received the same warning.
Well that's a pretty basic requirement that you needed to satisfy.
Obviously you also need to re-generate your .tpr from the new .mdp.
That'd be the most likely reason for an *identical* output.
Have you done enough background reading (e.g. wiki page on Carbon
Nanotube simulations) and/or gotten some experience with normal GROMACS
simulations?
Mark
>> Date: Mon, 21 Sep 2009 16:56:48 +1000
>> From: Mark Abraham <mark.abra...@anu.edu.au>
>> Subject: Re: [gmx-users] 1-4 interaction between atoms in PBC mode
>> To: Discussion list for GROMACS users <gmx-users@gromacs.org>
>> Message-ID: <4ab723b0.6040...@anu.edu.au>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>> Darrell Koskinen wrote:
>>
>>> Dear GROMACS-ians,
>>> I have created an infinite graphene sheet and upon running grompp, I
>>> get the following response:
>>>
>>> /Warning: 1-4 interaction between 10085 and 10445 at distance 19.679
>>> which is larger than the 1-4 table size 1.000 nm
>>> Warning: 1-4 interaction between 9244 and 9963 at distance 19.553
>>> which is larger than the 1-4 table size 1.000 nm
>>> These are ignored for the rest of the simulation
>>> This usually means your system is exploding,
>>> if not, you should increase table-extension in your mdp file
>>> These are ignored for the rest of the simulation/
>>>
>>> I assume that atoms from opposite ends of the simulation box are
>>> being seen by GROMACS as being 1-4 neighbors as a result of the PBC,
>>> but the shortest distance between the atoms is not being observed. Is
>>> this the problem? Is this problem resulting in the system exploding?
>>> And, how do I resolve this problem?
>>>
>>
>> Did you use periodic_molecules = yes in your .mdp file?
>>
>> Mark
>>
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
